As Greg said, the ball is completely in Disney and Marvel's court, probably more Disney's than Marvel's, and it doesn't hurt where things stand. Disney was going to save the last 6 episodes of Season 2 for sweeps month anyway. At least now Sony is not involved and if a third season is commissioned, Disney does not have to worry about splitting profits with Sony or interacting with Sony on this regard. I can imagine the deal between the two was that Sony wanted more control over the film franchise that they already have made 3 films with and are in production over a 4th and in exchange Disney gets the TV rights.
If the ratings for sweeps for the end of Season 2 prove promising, Disney may be willing to invest in a new season. For petty corporate reasons it could be possible that they may want to start over from scratch in some 1-2 years with a production team that wasn't pre-picked by Sony. For logical commercial reasons, it would be faster, cheaper, and quicker to syndication episode count to simply continue a series that only ended production earlier this year. Especially as this series is already selling DVD's, already selling toys, and is probably way more of a presence than the 2003 MTV series was. It also is doing very well in Canada, although I am not sure that matters much. International reception did help WOLVERINE AND THE X-MEN, though. Canada's YTV would lap up more SS-M YESTERDAY.
There is a part of me that is thinking that so long as the ratings for sweeps for the end of the season are healthy (that is, above average or show positive growth every week), Disney may bite for at least another 13 episodes, if not 26 to push it to 52 episodes, which is the low end of "syndication number" i.e. X-MEN EVOLUTION. Networks are usually happier with some 50-65 episodes to air in reruns for a while, i.e. TEEN TITANS on Boomerang or Cartoon Network (and even briefly Kid's WB). The fact that Disney owns Marvel and the cartoon is THEIRS now leads me to believe there is some chance that so long as it seems like a viable asset, Disney will consider pushing it since it is all THEIRS now. Again, it just seems to be the more logical choice in terms of cost and timing. It isn't as if Disney wasn't interested at all in the show. They outbid CW 4KIDS for airing rights. Whether they have been slow to air new episodes or not, they HAVE been airing reruns a gazillion times. It isn't like they aired the episodes 1-2-3 and then banished it, like FoxKids did with SPIDER-MAN UNLIMITED. That was a terrible show, but again, that merely was an example of a network airing an episode of a series once and then ditching it ASAP if they are not interested. Disney was interested in SS-M before and should continue to be now that Sony has backed off from it.
Even commissioning another 13-26 episodes of SS-M is a bargain for Disney, as they didn't have to pay a dime to produce the first 26 episodes, merely to air them. If anything, this is the best of many worlds for Disney. It surely can't cost more to continue an acquired series than to produce one from the foundation up. Disney has stepped off their "3D CGI animation or bust" self imposed rule with feature films mostly not because they realize crappy writing and celebrity casting will make or break ANY film, but because 2D animation is faster and cheaper than computer CGI and they can't afford so many bombs either. Hopefully this sort of shrewd shift for costs helps SS-M garner a 3rd season.
Again, while that would mean a gap between Season 2 and 3, but that might be timely if a 3rd season is airing just when hype for SM4 is bubbling.